R Observatory: Metrics for POINT version 1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

POINT

1.4Package record

Protein Structure Guided Local Test

0packages depend

6.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Shannon T. HollowayCRAN page ↗

Provides an implementation of a rare variant association test that utilizes protein tertiary structure to increase signal and to identify likely causal variants. Performs structure-guided collapsing, which leads to local tests that borrow information from neighboring variants on a protein and that provide association information on a variant-specific level. For details of the implemented method see West, R. M., Lu, W., Rotroff, D. M., Kuenemann, M., Chang, S-M., Wagner M. J., Buse, J. B., Motsinger-Reif, A., Fourches, D., and Tzeng, J-Y. (2019) doi:10.1371/journal.pcbi.1006722.

Changes in 1.4

Changes:

Added author@R field in DESCRIPTION

From NEWS in the release

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("POINT", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-point

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-POINT

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-POINT

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 1.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.4

READMENoVignettesNoNEWSYes · 33% structured · mentions 1.4Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 1
Examples that run: 100%1 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

6.1K

CRAN downloads in the past year

Rank #10,294 · ~17/day · ~507/mo

Releases R versions

Daily download trend is not available in this view yet.

36730 days

1K90 days

6.1K1 year

Compare downloads with other packages →

Also on72 r2u3 autocran

How downloads are counted

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Installing POINT adds 5 packages (4 with compiled code, 3.7 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppEigen 1.7 MB, RSpectra 125 KB.

Depends (5)

methodsstatsrARPACKMatrixCompQuadForm

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Shannon T. Holloway

Author, Maintainer since 1.1 (2019)

Rachel Marceau West

Author

Listed in earlier versions (2)

Holloway

no longer listed · 1.4

West

no longer listed · 1.4

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.4Latest
record
2025-05-04 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.3
record
2023-10-01 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2
record
2022-06-07 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.1
record
2019-03-05
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-03-05
Total releases: 4 / 7 yrs
License: GPL-2 OSI
Download size: 11 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("POINT")

Format

Holloway, S. T., & West, R. M. (2025). POINT: Protein Structure Guided Local Test (Version 1.4) [Computer software]. https://doi.org/10.32614/CRAN.package.POINT

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for POINT version 1.4 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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